You just need an understanding of Rhino. This is how loft works. For instance, lofts wont result in trimmed surfaces. So in your case of lofting a kinked top to a straight bottom, there is no way to make that shape without being a trimmed surface or a polysurface of two untrimmed surfaces. Rhino loft logic is set up the way of making untrimmed parts (easier to work with than trimmed surfaces) - So you can just Merge Coplanar faces on the loft.